SemBioProcess / SemGen

A tool for semantics-based annotation and composition of biosimulation models
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Ensure that curational metadata in models is preserved on roundtrips #297

Open maxneal opened 6 years ago

maxneal commented 6 years ago

The bug that was preventing SemGen from retaining some model-level annotations was fixed in 5cff2243563a09d6ef3aeabf1ea5e1ba54f4a603, but we need to develop a policy for determining which model-level annotations should be preserved when reading in a curated model from a repository. For example, we should probably keep an annotation that indicates the model's source publication, but probably not the dc:creator annotation, because when you export from SemGen, you're the new creator.

maxneal commented 6 years ago

We also need to talk to the BioModels curators to better understand which model-level annotations are valid, and thus, which we should preserve on export. We also need to determine whether we should create unique qualifiers so that we can store model-level annotations that use qualifiers that are also used in statements on individuals in SemSim OWL files (e.g. bqbiol:isVersionOf). My understanding is that an OWL object property can't be used simultaneously in an ontology-level annotation statement and in a statement on an OWL individual.

maxneal commented 3 years ago

Now that dc:creator and dc:contributor annotations on models should be supported in OMEX metadata, we should try to read in those annotations that exist in SBML models from BioModels.